Search

1. We present Visual TreeCmp—a package of applications for comparing phylogenetic tree sets. 2. Visual TreeCmp includes a graphical web interface allowing the visualization of compared trees and command line application extended by comparison methods recently proposed in the literature. 3. The phylogenetic tree similarity analysis in Visual TreeCmp can be performed using eighteen metrics, of which 11 are dedicated to rooted trees and seven to the un-rooted ones. Additionally, in the case of different sets of labels, the compared trees can be pruned so that the sets are identical. 4. The Visual TreeCmp is dedicated to people who need a universal and easy-to-use tool designed to compare arbitrary (not necessary binary) phylogenetic trees. An example of its use in a supertree accuracy analysis is described in section 3. 5. The Visual TreeCmp package Web application is available at: (https://eti.pg.edu.pl/TreeCmp), and its source codes available under the GNU license can be reached through several repositories located at: (https://github.com/TreeCmp)

New World bats represent over one third of global bat species and encompass the widest adaptive radiation among bats. Modern bat diversity in the Americas resulted from a mixture of migrations and colonisations of different taxa throughout the Cenozoic. Traditionally, these taxa are conceived as either South or North American, based on the location of their centres of diversification. To better understand the spatial and temporal processes behind modern biogeographic patterns of New World bat fauna, we investigated phylogenetic diversity (PD) and endemism (PE) for 325 American bat species using distribution maps and a species-level phylogenetic supertree of bats. Randomisation tests were used to evaluate the statistical significance of our results, and to derive a categorical analysis of neo- and palaeo-endemism (CANAPE) to deconstruct significant endemism into its different components. PD and PE showed different patterns than those previously reported for New World bats based on traditional measures of diversity. We found multiple centres of significant endemism across the New World for most bat families, extending the hypothesis of dual centres of diversification, previously proposed for Emballonuridae, Phyllostomidae and Mormoopidae, to Molossidae and Vespertilionidae. Our results indicate that Central America and southern North America played important roles in the diversification of New World bats, as did the Andes in the diversification of Vespertilionidae in South America. This article is protected by copyright. All rights reserved.

The rapid increase of molecular, as well as other types, of available classification data has created the need to combine this data into a uni-fied hypothesis. Supertree methods are essential when amalgamating phylogenetic information from various, possibly conflicting, sources into a single tree. The goal of a supertree algorithm is to satisfy maximally each such source of information in the output tree. Triplets, rooted trees over three leaves, are the minimal piece of such information when dealing with rooted trees. Due to its fundamental role in phylogenetics,extensive effort have been dedicated to several aspects regarding triplets’ research.We have devised a new tool, Triplet MaxCut (TMC), performing vari-ous operations in rooted supertree, principally amalgamating rooted trees based on amalgamating rooted triplets. The utility and efficiency of the algorithm is demonstrated by both simulation study and four real data supertree inputs. This article is protected by copyright. All rights reserved.

Ecologists frequently use a supertree method to generate phylogenies in ecological studies. However, the robustness of research results based on phylogenies generated with a supertree method has not been well evaluated. Here, we use the angiosperm tree flora of North America as a model system to test the robustness of phylogenies generated with a supertree method for studies on the relationship between phylogenetic properties and environment, by comparing the relationship between phylogenetic metrics and environmental variables derived from a phylogeny reconstructed with a supertree method to that derived from a phylogeny resolved at species level. North America was divided into equal area quadrats of 12 100 km2. Nine indices of phylogenetic structure were calculated for angiosperm tree assemblages in each quadrat using two phylogenies resolved at different levels (one resolved at the family level and the other resolved at the species level). Scores of phylogenetic indices were related to two major climatic variables (temperature and precipitation) using correlation and regression analyses. Scores of phylogenetic indices resulting from the two phylogenies are perfectly or nearly perfectly correlated. On average, there is no difference in the variation explained by the two climatic variables between scores of phylogenetic indices derived from the two phylogenies. Our study suggests that a phylogeny derived from a well resolved family-level supertree as backbone with genera and species attached to the backbone as polytomies is robust for studies investigating the relationship between phylogenetic structure and environment in biological assemblages at a broad spatial scale.

Relationships among taxonomic, functional, and phylogenetic dimensions of biodiversity provide insight about the relative contributions of ecological and evolutionary processes in structuring local assemblages. We used data for rodent species distributions from an extensive tropical elevational gradient to 1) describe elevational gradients for each of three dimensions of biodiversity, 2) evaluate the sufficiency of species richness as a surrogate for other dimensions, and 3) quantify the relative support for mechanisms that increase or decrease phylogenetic or functional dispersion. Taxonomic biodiversity was quantified by species richness, as well as by richness, evenness, diversity, dominance, and rarity at generic and familial levels. Morphological and categorical traits were used to estimate functional biodiversity, and an ultrametric mammalian supertree was used as the basis for estimating phylogenetic biodiversity. Elevational gradients of each dimension of biodiversity were strong, with significant linear and non-linear components based on orthogonal polynomial regression. Empirical linear and non-linear regression components were consistently different than those expected based on species richness for generic, familial, and phylogenetic biodiversity, but not for functional biodiversity. Nevertheless, the congruence of dimensions of biodiversity based on correlation analyses indicated that any one dimension is a useful surrogate for the other dimensions for rodents at Manu. Given variation in species richness, assemblages from lowland rainforests comprised more biodiversity than expected, whereas assemblages from cloud and elfin forests represented less biodiversity than expected. Warm temperatures, vertical complexity of the vegetation, and high productivity likely facilitate niche differentiation in rainforests, whereas cricetid rodents are competitively superior to other clades in the less structurally complex, less productive, and colder, high elevation habitats.

Aim To identify characteristics of a human-modified landscape that promote taxonomic (TD), functional (FD) and phylogenetic (PD) dimensions of bat biodiversity. Location Caribbean lowlands of northeastern Costa Rica. Methods During the dry and wet seasons, we quantified TD (Simpson's diversity), as well as FD and PD (Rao's quadratic entropy) of phyllostomid bat assemblages at 15 sites that represented a forest loss and fragmentation gradient. FD was estimated separately for each of seven functional components that reflect particular niche axes (e.g. diet, foraging strategy) and for all functional components combined (FDall). PD was based on relatedness of species derived from a supertree. We identified the best explanatory landscape characteristics of each dimension using hierarchical partitioning. Results Landscape effects were dimension and season specific. During the dry season, TD and PD increased with increasing proportions of pasture or size of forest patches, whereas FDall decreased with increasing size of forest patches. During the wet season, TD increased with increasing forest patch size, whereas FDall and PD increased with increasing compactness of forest patches and decreasing proximity. Decomposition of FD into separate functional components revealed different landscape effects on ecological aspects of assemblages. Main conclusions One dimension of biodiversity was not a good surrogate for another. Rather, decomposition of biodiversity into different dimensions and functional components facilitated identification of the aspects of assemblages that are most affected by forest conversion and fragmentation. Areas with intermediate amounts of forest and pasture during the dry season harboured highest diversity from taxonomic, functional and phylogenetic perspectives. During the wet season, areas with large, compact forest patches promoted the dimensions of biodiversity. Placement of areas with even amounts of forest and pasture adjacent to large, compact forest patches (e.g. reserves) may maintain high biodiversity of bats and the ecosystem functions that they provide throughout the year.

This study uses phylogeny-based measures of evolutionary potential (phylogenetic diversity and community structure) to evaluate the evolutionary value of vascular plant genera endemic to Chile. Endemicity is regarded as a very important consideration for conservation purposes. Taxa that are endemic to a single country are valuable conservation targets, as their protection depends upon a single government policy. This is especially relevant in developing countries in which conservation is not always a high resource allocation priority. Phylogeny-based measures of evolutionary potential such as phylogenetic diversity (PD) have been regarded as meaningful measures of the "value" of taxa and ecosystems, as they are able to account for the attributes that could allow taxa to recover from environmental changes. Chile is an area of remarkable endemism, harboring a flora that shows the highest number of endemic genera in South America. We studied PD and community structure of this flora using a previously available supertree at the genus level, to which we added DNA sequences of 53 genera endemic to Chile. Using discrepancy values and a null model approach, we decoupled PD from taxon richness, in order to compare their geographic distribution over a one-degree grid. An interesting pattern was observed in which areas to the southwest appear to harbor more PD than expected by their generic richness than those areas to the north of the country. In addition, some southern areas showed more PD than expected by chance, as calculated with the null model approach. Geological history as documented by the study of ancient floras as well as glacial refuges in the coastal range of southern Chile during the quaternary seem to be consistent with the observed pattern, highlighting the importance of this area for conservation purposes.

Summary 1. Research concerning spatial dynamics of biodiversity generally has been limited to considerations of the taxonomic dimension, which is insensitive to interspecific variation in ecological or evolutionary characteristics that play important roles in species assembly and provide linkages to ecosystem services. Consequently, the assumption that the taxonomic dimension is a good surrogate for other dimensions remains unconfirmed. 2. We assessed variation in taxonomic (species richness) as well as phylogenetic and functional (Rao’s quadratic entropy, a measurement of dispersion) dimensions of bat biodiversity along an elevational gradient in the Manu Biosphere Reserve of Peru. Phylogenetic dispersion was based on relatedness of species derived from a mammalian supertree. Functional dispersion was estimated separately for each of six functional components that reflect particular niche axes (e.g. diet, foraging strategy, body size) and for all functional components combined. 3. Species richness declined nonlinearly with elevation, whereas phylogenetic dispersion and functional dispersion based on all functional components were not significantly associated with elevation (orthogonal polynomial regression). Moreover, considerable heterogeneity in the form of elevational relationships existed among functional components. After accounting for variation in species richness, dispersion of phylogenetic, diet and foraging strategy attributes were significantly greater than expected at high elevations, whereas dispersion of body size was significantly less than expected at high elevations. 4. Species richness was a poor surrogate for phylogenetic or functional dispersion. Functional dispersion based on multiple components obscured patterns detected by particular components and hindered identification of mechanistic explanations for elevational variation in biodiversity. 5. Variation in phylogenetic dispersion effectively captured the composite variation represented by all functional components, suggesting a phylogenetic signal in functional attributes. 6. Mechanisms that give rise to variation in richness do not fully account for variation in phylogenetic or functional characteristics of assemblages. Greater than expected phylogenetic, diet and foraging strategy dispersion at high elevations were associated with the loss of phylogenetically or functionally redundant species, suggesting that increasing interspecific competition with decreasing productivity resulted in competitive exclusion. In contrast, low dispersion of size attributes at high elevations suggests the importance of abiotic filtering that favours small-sized species that can more easily enter torpor.

There are 26 phylogenetic studies for Bromeliaceae based on different sources of evidence. Despite thisbroadphylogeneticcoverageofBromeliaceae,however,theavailablephylogeneticdatadisplayascatteredsampling,with little overlap among different types of evidence. The aim of this study is to integrate the available phylogeneticinformation of the Bromeliaceae in one hypothesis using a supertree. To test which of them integrates best theinformation for Bromeliaceae, nine supertree methods were employed: Avcon, MSS, MinFlip, MMC, MRP,PhySIC_IST, Robinson–Foulds Supertree, Sfit, and SuperFine. Supertrees were compared with a reference tree,generated from the maximum likelihood (ML) analysis of a supermatrix integrated by 120 taxa of Bromeliaceae andsevencpDNAregions.Inordertoselectwhichmethodbestreconstructsthemostrobustphylogeny,twodifferentsetsofsourcetreeswereused:(i)thosegeneratedfromtheanalysisofeachindividualDNAregions;and(ii)fourselectedphylogenies (from the 26 publishedworks).We usedthe consensusfork index,normalized partitionmetric, patristicdistance coefficient, and the Shimodaira–Hasegawa test to compare supertrees with the reference tree. The bestperformingmethodswereusedtoconstructasupertreeusingallphylogeniesofBromeliaceae.TheSuperFinemethodgenerated the best supertree. The lack of overlapping among phylogenies was the major limiting factor for theintegration of the phylogenetic information of Bromeliaceae. Nonetheless, supertree methods helped in theidentification of poorly sampled groups, as well as to explore levels of agreement among published phylogeneticstudies for Bromeliaceae.Key words Bromeliaceae, cladistics, meta‐analysis, phylogenetic analysis, supermatrix, supertree.Bromeliaceae (Poales, Monocotyledoneae) is aNeotropical plant family that constitutes a monophy-letic group supported by strong molecular andmorphological synapomorphies (APG II, 2003). It isa highly diverse group (3346 species in 58 genera;Luther, 2012) and its members occur in environmentsrangingfromhyper‐humidtropicalrainorcloudforeststo the driest deserts (such as the Chilean AtacamaDesert), and from sea level up to 4200m. Plants can befound growing as terrestrials, epiphytes, or lithophytes(Smith & Downs, 1974, 1977, 1979).Traditionally, Bromeliaceae have been dividedintothreesubfamilies(Pitcairnioideae,Tillandsioideae,and Bromelioideae) that were distinguished by mor-phological characters of the flowers, fruits, and seeds(Mez,1896;SmithDSmith& Till, 1998). However, this view has been challengedby molecular studies. Based on a ndhF phylogeny,Givnishetal.(2007)establishedanewconceptofeightbromeliad subfamilies (Tillandsioideae, Bromelioi-deae, Brocchinioideae, Lindmanioideae, Hechtioideae,Puyoideae, Navioideae, and Pitcairnioideae s. str.)primarily characterized by the morphology of flowers,fruits, seeds, and molecular data (Givnish et al.,2007, 2011).There is a wealth of phylogenetic studies based onBromeliaceaethatincludetaxaatalltaxonomicalranks.Theseincludethegenus(i.e.,Almeidaetal.,2009;Sass& Specht, 2010), subfamily (Barfuss et al., 2005;Schulte et al., 2009), or family (Givnish et al., 2007,2011) levels. Evidence for these phylogenetic estima-tions spans all kinds of characters from basic

Question Variability in species function is often studied by using phylogenetic relatedness as a surrogate for functional similarity between species, rather than by measuring functional traits directly. The phylogenetic-based method is far less data-intensive than trait-based methods. However, to what extent community-level variability in species function is driven by phylogenetic history has rarely been explored in terms of composition and diversity. In this paper we test this empirically by asking: do differences in the functional composition and diversity of species assemblages (i.e. plots) along an environmental gradient mirror differences in phylogenetic structure? Location Coastal dune communities of the Tyrrhenian coast of Italy. Methods We calculated fuzzy-weighted mean trait values and the Rao index for dominant species in 405 plots using 16 functional traits that were measured in the field or from other sources. Based on a phylogenetic distance matrix among species obtained from an aged phylogenetic supertree, we applied matrix correlation tested against appropriate null models to calculate how much of the plot-to-plot variability in functional composition (measured through fuzzy weighting) and diversity (measured with the Rao index) is predicted by the corresponding phylogenetic metrics. Results At the species pool level there was evidence for a phylogenetic signal in trait variation. Furthermore, we found that differences in species functional diversity among plots were closely related to their phylogenetic variability, but this was not true for functional composition. Conclusions The results show that even when there is evidence of phylogenetic trait conservatism at the species pool level, phylogeny may be unable to capture all aspects of functional community structure. This emphasizes the need for caution when interpreting measures of phylogenetic community structure as proxies of functional community structure.

Extinction always results in loss of phylogenetic diversity (PD), but phylogenetically selective extinctions have long been thought to disproportionately reduce PD. Recent simulations show that tree shapes also play an important role in determining the magnitude of PD loss, potentially offsetting the effects of clustered extinctions. While patterns of PD loss under different extinction scenarios are becoming well characterized in model phylogenies, analyses of real clades that often have unbalanced tree shapes remain scarce, particularly for marine organisms. Here, we use a fossil-calibrated phylogeny of all living scleractinian reef corals in conjunction with IUCN data on extinction vulnerabilities to quantify how loss of species in different threat categories will affect the PD of this group. Our analyses reveal that predicted PD loss in corals varies substantially among different threats, with extinctions due to bleaching and disease having the largest negative effects on PD. In general, more phylogenetically clustered extinctions lead to larger losses of PD in corals, but there are notable exceptions; extinction of rare corals from distantly-related old and unique lineages can also result in substantial PD loss. Thus our results show that loss of PD in reef corals is dependent on both tree shape and the nature of extinction threats.

It has been proposed that supertree approaches should be applied to large multilocus datasets to achieve computational tractability. Large datasets such as those derived from phylogenomics studies can be broken into many locus-specific tree searches and the resulting trees can be stitched together via a supertree method. Using simulated data, workers have reported that they can rapidly construct a supertree that is comparable to the results of heuristic tree search on the entire dataset. To test this assertion with organismal data, we compare tree length under the parsimony criterion and computational time for 20 multilocus datasets using supertree (SuperFine and SuperTriplets) and supermatrix (heuristic search in TNT) approaches. Tree length and computational times were compared among methods using the Wilcoxon matched-pairs signed rank test. Supermatrix searches produced significantly shorter trees than either supertree approach (SuperFine or SuperTriplets; P 0.0002 in both cases). Moreover, the processing time of supermatrix search was significantly lower than SuperFine+locus-specific search (P 0.01) but roughly equivalent to that of SuperTriplets+locus-specific search (P 0.4, not significant). In conclusion, we show by using real rather than simulated data that there is no basis, either in time tractability or in tree length, for use of supertrees over heuristic tree search using a supermatrix for phylogenomics.

The demand for knowledge about the tree of life is steadily rising in ecology and other fields, but bioinformatic resources designed to meet these needs remain poorly developed. Ecologists pursuing phylogenetic insights into the organization of communities have come to rely on relatively conservative reference trees that, in general, are poorly resolved and documented. New methods for inferring very large trees by mining data from DNA sequence repositories will undoubtedly be useful in community phylogenetics, but are not without limitations. Here we argue that the collective phylogenetic knowledge embodied in the literature of systematics is a valuable resource that can be tapped in assembling synthetic trees. Assembling a composite ''literature-based'' tree by the judicious grafting of clades is one way to achieve a synthesis of current knowledge, and could, under some circumstances, better represent ''what we know'' about phylogenetic relationships than results obtained from automated pipelines. We describe an approach and new software for storing and annotating trees from published studies and grafting clades together in a documented and repeatable manner. Using this agglomerative approach, we are in the process of assembling a literature- based tree for land plants, which presently contains 14 423 species from over 259 sources. For this strategy to be maximally effective, improvements in digital infrastructure are needed to capture and deploy advances in phylogenetic knowledge as they are published.

Aim Phylogenetic diversity can provide insight into how evolutionary processes may have shaped contemporary patterns of species richness. Here, we aim to test for the influence of phylogenetic history on global patterns of amphibian species richness, and to identify areas where macroevolutionary processes such as diversification and dispersal have left strong signatures on contemporary species richness. Location Global; equal-area grid cells of approximately 10,000 km2. Methods We generated an amphibian global supertree (6111 species) and repeated analyses with the largest available molecular phylogeny (2792 species). We combined each tree with global species distributions to map four indices of phylogenetic diversity. To investigate congruence between global spatial patterns of amphibian species richness and phylogenetic diversity, we selected Faith’s phylogenetic diversity (PD) index and the total taxonomic distinctness (TTD) index, because we found that the variance of the other two indices we examined (average taxonomic distinctness and mean root distance) strongly depended on species richness. We then identified regions with unusually high or low phylogenetic diversity given the underlying level of species richness by using the residuals from the global relationship of species richness and phylogenetic diversity. Results Phylogenetic diversity as measured by either Faith’s PD or TTD was strongly correlated with species richness globally, while the other two indices showed very different patterns. When either Faith’s PD or TTD was tested against species richness, residuals were strongly spatially structured. Areas with unusually low phylogenetic diversity for their associated species richness were mostly on islands, indicating large radiations of few lineages that have successfully colonized these archipelagos. Areas with unusually high phylogenetic diversity were located around biogeographic contact zones in Central America and southern China, and seem to have experienced high immigration or in situ diversification rates, combined with local persistence of old lineages. Main conclusions We show spatial structure in the residuals of the relationship between species richness and phylogenetic diversity, which together with the positive relationship itself indicates strong signatures of evolutionary history on contemporary global patterns of amphibian species richness. Areas with unusually low and high phylogenetic diversity for their associated richness demonstrate the importance of biogeographic barriers to dispersal, colonization and diversification processes.

Pecnerova, P. & Martinkova, N. (2012). Evolutionary history of tree squirrels (Rodentia, Sciurini) based on multilocus phylogeny reconstruction. —Zoologica Scripta, 41, 211–219. Tree squirrels of the tribe Sciurini represent a group with unresolved phylogenetic relationships in gene trees. We used partial sequences of mitochondrial genes for 12S rRNA, 16S rRNA, cytochrome b and d-loop, and nuclear irbp, c-myc exon 2 and 3 and rag1 genes to reconstruct phylogenetic relationships within the tribe, maximizing the number of analysed species. Bayesian inference analysis of the concatenated sequences revealed common trends that were similar to those retrieved with supertree reconstruction. We confirmed congruence between phylogeny and zoogeography. The first group that diverged from a common ancestor was genus Tamiasciurus, followed by Palaearctic Sciurus and Indomalayan Rheithrosciurus macrotis. Nearctic and Neotropical Sciurus species formed a monophyletic group that included Microsciurus and Syntheosciurus. Neotropical Sciurini were monophyletic with a putative exception of Syntheosciurus brochus that was included in a polychotomy with Nearctic Sciurus in supertree analyses. Our data indicate that Sciurini tree squirrels originated in the northern hemisphere and ancestors of contemporary taxa attained their current distribution through overland colonization from the nearest continent rather than through trans-Pacific dispersal.

Taxonomic, morphological, and functional diversity are often discordant and independent components of diversity. A fundamental and largely unanswered question in evolutionary biology is why some clades diversify primarily in some of these components and not others. Dramatic variation in trunk vertebral numbers (14 to >300) among squamate reptiles coincides with different body shapes, and snake-like body shapes have evolved numerous times. However, whether increased evolutionary rates or numbers of vertebrae underlie body shape and taxonomic diversification is unknown. Using a supertree of squamates including 1375 species, and corresponding vertebral and body shape data, we show that increased rates of evolution in vertebral numbers have coincided with increased rates and disparity in body shape evolution, but not changes in rates of taxonomic diversification. We also show that the evolution of many vertebrae has not spurred or inhibited body shape or taxonomic diversification, suggesting that increased vertebral number is not a key innovation. Our findings demonstrate that lineage attributes such as the relaxation of constraints on vertebral number can facilitate the evolution of novel body shapes, but that different factors are responsible for body shape and taxonomic diversification.

Aim We evaluate the extent to which the tropical conservatism hypothesis can explain the evolutionary development of the Muscidae. Furthermore, we compare the geographical patterns of muscid phylogenetic structure with biogeographical regions that have been identified for Neotropical insects. Location Central and South America. Methods We modelled the geographic distributions of 658 species using Maxent and 19 environmental variables. A generic-level supertree of the Muscidae was assembled using matrix representation with parsimony and used to map the geographic pattern of mean root distance (MRD), a metric of the relative evolutionary development of assemblages. Regression models (ordinary least squares and regression trees) were used to examine temperature and other environmental correlates of MRD to explore potential environmental drivers of muscid diversification. We used the regression tree results to recognize variable intervals that best explained MRD, and these intervals were mapped to recognize and compare with biogeographical regions of Neotropical insects. Results The geographic pattern of MRD was consistent with the tropical conservatism hypothesis: species in genera that diversified relatively early, as measured by their distance from the tree root, dominate lowland tropical South America, whereas species in genera that diversified more recently occupy extra-tropical areas, sub-Antarctic areas and the Andean highlands. Temperature was the strongest correlate of MRD. Three biogeographical regions were recognized and they coincided with two regions known for insects. Main conclusions Evolutionary responses of muscid flies to post-Eocene climate change taking the form of an expansion of a tropical group into regions with colder climates may be fundamental to explaining their distribution in the Neotropics. Our biogeographical regions delimited by temperature and the phylogenetic metric, surrogates of the tropical conservatism hypothesis, were very similar to general insect patterns, supporting the ‘tropical origin and evolutionary response to climate cooling’ as a broadly based historical narrative for the Neotropics.

The Parareptilia are a small but ecologically and morphologically diverse clade of Permian and Triassic crown amniotes generally considered to be phylogenetically more proximal to eureptiles (diapsids and their kin) than to synapsids (mammals and their kin). A recent supertree provides impetus for an analysis of parareptile diversity through time and for examining the influence of the end- Permian mass extinction on the clade’s origination and extinction rates. Phylogeny-corrected measures of diversity have a significant impact on both rates and the distribution of origination and extinction intensities. Time calibration generally results in a closer correspondence between origination and extinction rate values than in the case of no time correction. Near the end-Permian event, extinction levels are not significantly higher than origination levels, particularly when time calibration is introduced. Finally, regardless of time calibration and ⁄ or phylogenetic correction, the distribution of rates does not differ significantly from unimodal. The curves of rate values are discussed in the light of the numbers and distributions of both range extensions and ghost lineages. The disjoint time distributions of major parareptile clades (e.g. procolophonoids and nycteroleterids-pareiasaurs) are mostly responsible for the occurrence of long-range extensions throughout the Permian. Available data are not consistent with a model of sudden decline at the end-Permian but rather suggest a rapid alternation of originations and extinctions in a number of parareptile groups, both before and after the Permian ⁄ Triassic boundary.

Summary 1. Unresolved nodes in phylogenetic trees (polytomies) have long been recognized for their influences on specific phylogenetic metrics such as topological imbalance measures, diversification rate analysis and measures of phylogenetic diversity. However, no rigorously tested, biologically appropriate method has been proposed for overcoming the effects of this phylogenetic uncertainty. 2. Here, we present a simple approach to polytomy resolution, using biologically relevant models of diversification. Using the powerful and highly customizable phylogenetic inference and analysis software beast and r, we present a semi-automated ‘polytomy resolver’ capable of providing a distribution of tree topologies and branch lengths under specified biological models. 3. Utilizing both simulated and empirical data sets, we explore the effects and characteristics of this approach on two widely used phylogenetic tree statistics, Pybus’ gamma (γ) and Colless’ normalized tree imbalance (Ic). Using simulated pure birth trees, we find no evidence of bias in either estimate using our resolver. Applying our approach to a recently published Cetacean phylogeny, we observed the expected small positive bias in γ and decrease in Ic. 4. We further test the effect of polytomy resolution on diversification rate analysis using the Cetacean phylogeny. We demonstrate that using a birth–death model to resolve the Cetacean tree with 20%, 40% and 60% of random nodes collapsed to polytomies gave qualitatively similar patterns regarding the tempo and mode of diversification as the same analyses on the original, fully resolved phylogeny. 5. Finally, we applied the birth–death polytomy resolution approach to a large (>5000 tips), but unresolved, supertree of extant mammals. We report a distribution of fully resolved model-based trees, which should be useful for many future analysis of the mammalian supertree.

New inference techniques, such as supertrees, have improved the construction of large phylogenies, helping to reveal the tree of life. In addition, these large phylogenies have enhanced the study of other evolutionary questions, such as whether traits have evolved in a neutral or adaptive way, or what factors have influenced diversification. However, supertrees usually lack branch lengths, which are necessary for all these issues to be investigated. Here, divergence times within the largest family of flowering plants, namely the Asteraceae, are reviewed to estimate time-calibrated branch lengths in the supertree of this lineage. An inconsistency between estimated dates of basal branching events and the earliest asteraceous fossil pollen record was detected. In addition, the impact of different methods of branch length assignment on the total number of transitions between states in the reconstruction of sexual system evolution in Asteraceae was investigated. At least for this dataset, different branch length assignation approaches influenced maximum likelihood (ML) reconstructions only and not Bayesian ones. Therefore, the selection of different branch length information is not arbitrary and should be carefully assessed, at least when ML approaches are being used. The reviewed divergence times and the estimated time-calibrated branch lengths provide a useful tool for future phylogenetic comparative and macroevolutionary studies of Asteraceae.

Klug, S. & Kriwet, J. (2010). Timing of deep-sea adaptation in dogfish sharks: insights from a supertree of extinct and extant taxa. —Zoologica Scripta, 39, 331–342. Dogfish sharks (Squaliformes) constitute a monophyletic group of predominantly deep-water neoselachians, but the reasons and timing of their adaptation to this hostile environment remain ambiguous. Late Cretaceous dogfish sharks, which generally would be associated with deep-water occur predominantly in shallow water environments. Did the end-Cretaceous mass extinction event that eliminated large numbers of both terrestrial and aquatic taxa and clades including sharks trigger the evolutionary adaptation of present deep-water dogfish sharks? Here, we construct, date, and analyse a genus-level phylogeny of extinct and living dogfish sharks to bring a new perspective to this question. For this, eleven partial source trees of dogfish shark interrelationships were merged to create a comprehensive phylogenetic hypothesis. The resulting supertree is the most inclusive estimate of squaliform interrelationships that has been proposed to date containing 23 fossil and extant members of all major groups. †Eoetmopterus represents the oldest dalatoid. †Microetmopterus, †Paraphorosoides, †Proetmopterus and †Squaliogaleus are stem-group dalatoids in which bioluminescence most likely was not developed. According to our analyses, bioluminescence in dogfish sharks was already developed in the early Late Cretaceous indicating that these sharks adapted to deep-water conditions most likely at about 100 Mya. The advantage of this reconstruction is that the fossil record is used directly for age node estimates rather than employing molecular clock approaches.

We present the first phylogenies to include all extant species of Perissodactyla (oddtoed hoofed mammals) and the recently extinct quagga (Equus quagga). Two independent data sets were examined; one based on multiple genes and analyzed using both supertree and supermatrix approaches, and a second being a supertree constructed from trees collected from the scientific literature. All methods broadly confirmed the traditional view of perissodactyl interfamily relationships, with Equidae (¼ Hippomorpha) forming the sister-group to the clade Rhinocerotidae þ Tapiridae (¼ Ceratomorpha). The contentious affinity of the Sumatran rhino (Dicerorhinus sumatrensis) is resolved in favour of it forming a clade with the two Asian rhinos (genus Rhinoceros). However, no data set or tree-building method managed to satisfactorily resolve the historically contentious relationships among extant equids; little agreement appears among the different trees for this group. In general, both the supertree and supermatrix approaches performed equally well, but both were hindered by the current paucity of data (e.g. no single gene has been sequenced to date for all 17 species) and its patchy distribution within Equidae. More data, both molecular and morphological, are required for all species to resolve the poorly supported nodes.

The fowls (Anseriformes and Galliformes) comprise one of the major lineages of birds and occupy almost all biogeographical regions of the world. The group contains the most economically important of all bird species, each with a long history of domestication, and is an ideal model for studying ecological and evolutionary patterns. Yet, despite the relatively large amount of systematic attention fowls have attracted because of their socio-economic and biological importance, the species-level relationships within this clade remain controversial. Here we used the supertree method matrix representation with parsimony to generate a robust estimate of species-level relationships of fowls. The supertree represents one of the most comprehensive estimates for the group to date, including 376 species (83.2% of all species; all 162 Anseriformes and 214 Galliformes) and all but one genera. The supertree was well-resolved (81.1%) and supported the monophyly of both Anseriformes and Galliformes. The supertree supported the partitioning of Anseriformes into the three traditional families Anhimidae, Anseranatidae, and Anatidae, although it provided relatively poor resolution within Anatidae. For Galliformes, the majority-rule supertree was largely consistent with the hypothesis of sequential sister-group relationships between Megapodiidae, Cracidae, and the remaining Galliformes. However, our species-level supertree indicated that more than 30% of the polytypic genera examined were not monophyletic, suggesting that results from genus-level comparative studies using the average of the constituent species’ traits should be interpreted with caution until analogous species-level comparative studies are available. Poorly resolved areas of the supertree reflect gaps or outstanding conflict within the existing phylogenetic database, highlighting areas in need of more study in addition to those species not present on the tree at all due to insufficient information. Even so, our supertree will provide a valuable foundation for understanding the diverse biology of fowls in a robust phylogenetic framework.

Sociality in insects may negatively impact on species richness. We tested whether termites have experienced shifts in diversification rates through time. Supertree methods were used to synthesize family-level relationships within termites, cockroaches and mantids. A deep positive shift in diversification rate is found within termites, but not in the cockroaches from which they evolved. The shift is responsible for most of their extant species richness suggesting that eusociality is not necessarily detrimental to species richness, and may sometimes have a positive effect. Mechanistic studies of speciation and extinction in eusocial insects are advocated.

Whereas previous studies have investigated correlates of extinction risk either at global or regional scales, our study explicitly models regional effects of anthropogenic threats and biological traits across the globe. Using phylogenetic comparative methods with a newly-updated supertree of 5020 extant mammals, we investigate the impact of species traits on extinction risk within each WWF ecoregion. Our analyses reveal strong geographical variation in the influence of traits on risk: notably, larger species are at higher risk only in tropical regions. We then relate these patterns to current and recent-historical human impacts across ecoregions using spatial modelling. The body-mass results apparently reflect historical declines of large species outside the tropics due to large-scale land conversion. Narrow-ranged and rare species tend to be at high risk in areas of high current human impacts. The interactions we describe between biological traits and anthropogenic threats increase understanding of the processes determining extinction risk.

8 páginas, 2 figuras, 2 tablas., With the advent of molecular phylogenies the assessment of community assembly processes has become a central topic in community ecology. These processes have focused almost exclusively on habitat filtering and competitive exclusion. Recent evidence, however, indicates that facilitation has been important in preserving biodiversity over evolutionary time, with recent lineages conserving the regeneration niches of older, distant lineages. Here we test whether, if facilitation among distant-related species has preserved the regeneration niche of plant lineages, this has increased the phylogenetic diversity of communities. By analyzing a large worldwide database of species, we showed that the regeneration niches were strongly conserved across evolutionary history. Likewise, a phylogenetic supertree of all species of three communities driven by facilitation showed that nurse species facilitated distantly related species and increased phylogenetic diversity., We thank D. Ackerly, J. Bascompte, R.M. Callaway, R. Cruz, T. Fukami, P. García-Fayos, P. Jordano, J. Pausas and E. Rezende, and three anonymous referees for comments on the ideas conveyed in this article. A. Vital, J.P. Castillo, C. Rodríguez, and M. Morales helped with field samplings. Our research is funded by DGAPA-UNAM, Project IN227605, and Programa Iberoamericano de Ciencia y Tecnología para el Desarrollo, Subprograma Diversidad Biológica (Project XII-6) for travel expenses to A.V.-B.

The reproductive strategies of frogs are highly diverse, but analysis of these strategies in a phylogenetic context has lagged behind other taxa. Here we investigate associations between aspects of parental care and egg size in a phylogenetic context. We obtained data on egg size and parental care strategies in various species of frogs from the scientific literature. We developed a phylogenetic supertree of frogs by combining the results of multiple phylogenetic analyses using matrix representation parsimony. We used phylogenetic pairwise comparisons to investigate the correlation between various forms of parental care and egg size across the order Anura. We also investigated correlations between tadpole carnivory and egg size, and phytotelm breeding and egg size. We also investigated the association of egg size with several environmental factors. Parental care, male parental care, direct development, stream breeding and montane breeding habitats were all associated with large egg size. Female care (in species with trophic egg feeding), carnivory, use of small pools (phytotelmata) and use of temporary pools were not associated with egg size.

Collectively, ray-finned fishes (Actinopterygii) display far more diversity in many reproductive and genomic features than any other major vertebrate group. Recent large-scale comparative phylogenetic analyses have begun to reveal the evolutionary patterns and putative causes for much of this diversity. Several such recent studies have offered clues to how different reproductive syndromes evolved in these fishes, as well as possible physiological and genomic triggers. In many cases, repeated independent origins of complex reproductive strategies have been uncovered, probably reflecting convergent selection operating on common suites of underlying genes and hormonal controls. For example, phylogenetic analyses have uncovered multiple origins and predominant transitional pathways in the evolution of alternative male reproductive tactics, modes of parental care and mechanisms of sex determination. They have also shown that sexual selection in these fishes is repeatedly associated with particular reproductive strategies. Collectively, studies on reproductive and genomic diversity across the Actinopterygii illustrate both the strengths and the limitations of comparative phylogenetic approaches on large taxonomic scales.

Using supertree phylogenetic reconstructions, we investigate how livebearing and freshwater adaptations may have shaped evolutionary patterns in the Atherinomorpha, a large clade (approximately 1500 extant species) of ray-finned fishes. Based on maximum parsimony reconstructions, livebearing appears to have evolved at least four times independently in this group, and no reversions to the ancestral state of oviparity were evident. With respect to habitat, at least five evolutionary transitions apparently occurred from freshwater to marine environments, at least two transitions in the opposite direction, and no clear ancestral state was identifiable. All viviparous clades exhibited more extant species than their oviparous sister taxa, suggesting that transitions to viviparity may be associated with cladogenetic diversification. Transitions to freshwater were usually, but not invariably associated with increased species richness, but the trend was, overall, not significant among sister clades. Additionally, we investigated whether livebearing and freshwater adaptations are currently associated with elevated risks of extinction as implied by species' presence on the 2004 IUCN Red List. Despite being correlated with decreased brood size, livebearing has not significantly increased extinction risk in the Atherinomorpha. However, freshwater species were significantly more likely than marine species to be listed as endangered.

instead of using matrices and automated tree-building programs. We present an estimate of the phylogenetic relationships of 1723 extant and one extinct species of oscine passerine birds (Aves: Passeri) — more than 37% of the total. We included 34/35 (97%) families, 38/39 (97%) subfamilies and 40/43 (93%) tribes. Overall resolution is 83% of a fully bifurcating tree. The basal lineages are all distributed in the Australo-Papuan region, but several more distal lineages dispersed out of this region and radiated in other parts of the world. However, taxa of the Australian region suffer from larger evolutionary gaps and the deep branches of the Sylvioidea and nine South American primaried oscines are still poorly resolved.

Aim To determine whether life-history characters that affect population persistence (e.g. habit and life span) and those that influence reproductive success (e.g. sexual system and fruit type) are non-randomly correlated with extinction risk (i.e. threat category) in the Australian flora (c. 19,000 species, of which c. 14% is threatened). To identify patterns that present useful conservation directions. To understand patterns of extinction risk in the Australian flora at a broad scale. Location Continental Australia. Methods A country-wide exploration of four life-history characters in the Australian flora (n = 18,822 species) was undertaken using reference texts, expert opinion, herbarium records and field work. For each character and threat-category combination, a G-test (using a log-linear model) was performed to test the null hypothesis that the two factors were independent in their effects on count. A generalized linear model (GLM) with a logit link and binomial error distribution was constructed with the proportion of taxa in each extinction risk category as the response variable and the habit, sex and fruit-type characters as explanatory terms. In a separate approach, we investigated patterns across the threat categories of non-endangered extant, endangered, and extinct using a multinomial model. We examined whether or not species-poor genera were more likely to contain threatened or extinct species than species-rich genera. A GLM with a binomial error distribution and logit link function was constructed to obtain a weighted regression on the proportion of species listed as extinct or endangered within a genus versus the log of the size of the genus. We also used a supertree analysis and character tracing to investigate the role of phylogeny on extinction risk. Results We found that the Australian flora is primarily composed of bisexual shrubs with dry-dehiscent fruits. Dioecious breeding systems (separate female and male flowers on separate plants) in many floras are the predominant unisexual system, but in Australia there are unexpectedly high levels of monoecy (separate female and male flowers on the same plant). Within the extinct data set of 31 species we detected a significant departure from that expected for habit but not for life span, sexual system or fruit type. There are significantly fewer trees on the extinct list than expected. This may reflect the greater resilience of trees than of other growth habits to extinction processes as well as the observation time-frame. Within the endangered data set of 450 species we found significant differences in the representation of the observed characters from that expected within sex systems and fruit types. We show that, depending on the life form, unisexual breeding systems can be significantly and positively associated with endangered species compared with non-threatened species. For example, there are more monoecious species than expected by chance among the tree species listed as endangered but fewer among the herbaceous life forms. Threat category was found to be non-randomly clustered in some clades. Main conclusions Life-history characters in certain combinations are predictive of extinction risk. Phylogeny is also an important component of extinction risk. We suggest that specific life-history characters could be used for conservation planning and as an early warning sign for detecting vulnerability in lists of species.

Digital maps and a dated supertree of global carnivore species were used to assess the distribution of American carnivores’ phylogenetic diversity (PD, measured in millions of years) both from a geopolitical perspective (‘evolutionary heritage’ or EH) and on the basis of species’ range size and conservation status. A new measure, range-weighted EH, is introduced. This measure partitions the total PD of the tree between countries based on the proportion of species’ ranges within each country. Sociopolitical correlates of these measures were explored. Only 3% of the total PD in the Americas is endemic to any one country. As expected, the measures of PD are positively correlated with each other and with species richness. The USA contains the most species, the most EH and the second most range-weighted EH after Brazil. Indeed, larger and richer countries, and those with the lowest state-corruption-rate hold most EH. No significant differences were observed in the amount of PD remaining if species are removed at random, or following more plausible sequences based on IUCN conservation status and range size. Eighty percent of the American carnivores’ PD would remain safe if only the set of not threatened species were to remain. Roughly the same is true if only the 50% most widespread species were to persist. Samples of wide-ranging species represent more of the entire tree than do samples of narrow-ranging species, highlighting the importance of the former for conservation strategies. We suggest that similar approaches be applied to more groups across the globe to assess which countries and areas steward the most PD, as well as which species and taxa do, in order to plan conservation actions consequently.

Comparative studies require information on phylogenetic relationships, but complete species-level phylogenetic trees of large clades are difficult to produce. One solution is to combine algorithmically many small trees into a single, larger supertree. Here we present a virtually complete, species-level phylogeny of the marsupials (Mammalia: Metatheria), built by combining 158 phylogenetic estimates published since 1980, using matrix representation with parsimony. The supertree is well resolved overall (73.7%), although resolution varies across the tree, indicating variation both in the amount of phylogenetic information available for different taxa, and the degree of conflict among phylogenetic estimates. In particular, the supertree shows poor resolution within the American marsupial taxa, reflecting a relative lack of systematic effort compared to the Australasian taxa. There are also important differences in supertrees based on source phylogenies published before 1995 and those published more recently. The supertree can be viewed as a meta-analysis of marsupial phylogenetic studies, and should be useful as a framework for phylogenetically explicit comparative studies of marsupial evolution and ecology.

Most studies of exotic species invasions only consider the factors that affect the establishment of populations following release, yet this is only one step on the invasion pathway. Different factors are likely to influence which species are transported and released. Here, we examine the influence of species traits on the successful transition of species through several stages in the introduction pathway (transport, release, and establishment), using parrots (Aves: Psittaciformes) as a model system. We use a species-level supertree of parrots to test for phylogenetic auto-correlation in the introduction process. Our analyses find that different sets of variables are related to the probability that a species enters each stage on the invasion pathway. The availability of individuals for transport and release seems to be most important for passage through these stages, but has no obvious effect on establishment following release. Rather, establishment success is higher for sedentary species, and species with broad diets.

The first MRP (matrix representation with parsimony) supertree phylogeny of the Lipotyphla is presented, covering all the families that were considered to make up the traditional mammalian order Insectivora. The phylogeny does not examine relationships within the shrew subfamily Crocidurinae, but all other taxa are considered at the species level, drawing upon 41 years of systematic literature and combining information from 47 published sources. The MRP technique is also critically discussed. This study will be of use to comparative biology studies of the Lipotyphla (or of mammals as a whole) and is a rigorous review of past systematic work, as well as clearly demonstrating our current level of knowledge. The supertree clearly details a strong imbalance in phylogenetic understanding across the taxon: a great deal is known about the hedgehogs and gymnures (Erinaceidae), the New World moles (Talpidae), Palaearctic species of Sorex (subgenus Sorex )a nd the relationships between genera of red-toothed shrews (Soricinae). The supertree, however, clearly shows areas where our knowledge is conflicting or non-existent, and these gaps do not always correspond to obscure species: nothing is known about the systematics of Old World mole genera. Also very little is known about golden moles (Chrysochloridae) and the shrew-tenrec genus Microgale ,s ome of the most threatened mammals on Earth.

The evolutionary theory of aging predicts that life span should decrease in response to the amount of mortality caused by extrinsic sources. Using this prediction, we selected six life history and ecological factors to use in a comparative analysis of longevity among 64 bat species. On average, the maximum recorded life span of a bat is 3.5 times greater than a non-flying placental mammal of similar size. Records of individuals surviving more than 30 years in the wild now exist for five species. Univariate and multivariate analyses of species data, as well as of phylogenetically independent contrasts obtained using a supertree of Chiroptera, reveal that bat life span significantly increases with hibernation, body mass and occasional cave use, but decreases with reproductive rate and is not influenced by diet, colony size or the source of the record. These results are largely consistent with extrinsic mortality risk acting as a determinant of bat longevity. Nevertheless, the strong association between life span and both reproductive rate and hibernation also suggests that bat longevity is strongly influenced by seasonal allocation of non-renewable resources to reproduction. We speculate that hibernation may provide a natural example of caloric restriction, which is known to increase longevity in other mammals.

A method to calculate semi-strict supertrees is proposed. The semi-strict supertrees are calculated by creating the matrix that represents all the groups in the source trees (as done in already existing techniques), and then finding the trees determined by the ultra-clique. The ultra-clique is defined as the set of characters where each possible subset is compatible with each possible subset from the entire matrix. Finding the ultra-clique is computationally complex (since in most cases many of the characters have missing entries), but a heuristic method yields reliable results. When the trees have no conflict, or when there are only two trees, the method produces the exact result for any ordering of the input trees and any ordering of the groups within them; when there are more than two trees and they have conflict, a single ordering or sequence can create some spurious groups, but doing multiple sequences eliminates the spurious groups. The method uses only state set operations, and is thus easily implemented in computer programs. Unlike any existing type of supertree, semi-strict supertrees display all the groups, and only those groups, that are implied by at least some combination of the input trees and contradicted by none. The idea that supertrees should take into account the number of occurences of a given group, so as to retain some groups even in the case of conflict, is discussed; it is argued that a conceptual equivalent of the majority rule consensus is not possible when the sets of taxa differ among trees. Also, when pruning taxa from a set of trees, the supertree can display groups that contradict the consensus for the entire trees, suggesting that supertrees for matrices with very dissimilar sets of taxa should be interpreted with caution. If (for any valid reason) the data cannot be combined in a single matrix, it is advisable that the taxon sets in the matrices be as similar as possible. © 2002 Elsevier Science (USA). All rights reserved. Fil: Goloboff, Pablo Augusto. Universidad Nacional de Tucumán; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Pol, Diego. American Museum of Natural History; Estados Unidos

During the last decades, gene trees have been often interpreted as species phylogenies. However, the extensive gene tree discordance found in multi-locus datasets has put into question this interpretation, and a variety of new methods that explicitly consider species trees have been proposed in recent years. Some of these explicitly consider evolutionary processes that can lead to true gene tree discordance, namely incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. Choosing the most appropriate species tree method for the data at hand is not straightforward due to different data prerequisites, model assumptions, analytical strategies and computational implementations. Key Concepts: We could think of at least three different phylogenetic layers corresponding to species trees, locus trees and gene trees. These depict, respectively, the history of the sampled species, loci and genes copies. Traditional phylogenetic inference has focused on the reconstruction of gene trees, assumed to be accurate proxies for species history. True species, locus and gene trees can be incongruent due to the effect of evolutionary processes like incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. This incongruence might appear larger due to estimation error. Extensive gene tree incongruence unveiled in multi-locus datasets has encouraged the development of methods that explicitly reconstruct species trees. The supermatrix approach combines loci into a super-alignment and estimates the corresponding supergene tree. Supertree methods combine gene trees to obtain an estimate of the species tree. Other methods co-estimate gene and species trees in a single step using full probabilistic models. Different species tree methods require distinct data specifications, mainly related with the consideration of paralogs, number of sampled species, missing taxa and number of loci. Rooting and reconstruction uncertainty must be carefully considered before choosing a species tree method. Keywords: supermatrix; supertree; incomplete lineage sorting; gene duplication and loss; horizontal gene transfer; hybridisation; multispecies coalescent; reconciliation

Fire may act as a selective force on plants both through its direct effects by killing or wounding susceptible individuals and through its effect on the environment: the post-fire environment may select specific physiological traits or life histories. We used phylogenetic independent contrasts to test the hypothesis that fire has selected for correlated evolution among alternative suites of traits in pines: a survival/avoidance suite characterized by thick bark, height, and self-pruning of dead branches; and a fire-embracing strategy in which plants invest little into survival, exhibit traits which enhance flammability, and use fire as a means to cue seedling establishment to the post-fire environment through serotinous cones. We created a set of alternative ‘supertree’ phylogenies for the genus Pinus from published sources. Using these alternative phylogenies, published ecological data for 38 pine species, and newly collected morphological data, we demonstrate that much variation in trait evolution occurs along a fire-surviving/fire-embracing axis. Pines vary in their susceptibility to ignition since a tree that retains dead branches is more likely to carry a fire into the canopy than a tree that self-prunes. The evolution of increased flammability may have altered evolutionary trajectories prompting an evolutionary switch from a fire-surviving to a fire-embracing life history. Alternatively, the fire-embracing strategy may in fact select for increased flammability to ensure canopy ignition and the realization of serotinous seed-release.

Phylomatic (http://www.phylodiversity.net/phylomatic) is an online phylogenetic query tool where users submit a list of taxa (e.g. from an ecological community), with modern family and genus names, and which returns a phylogenetic hypothesis for the relationships among taxa. Any set of stored phylogenies, or a user-supplied one, can be chosen as the basis for the returned phylogeny, and several output formats for the tree can be selected. Currently, the source databases cover seed plants.

Summary Baum, B. R.: Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. - Taxon 41: 3-10. 1992. - ISSN 0040-0262. A procedure of combining trees obtained from data sets of different kinds, similar to Brooks's technique but for a different purpose, with the aim of combining these data sets, is detailed along with examples used in five unrepeated combinations from a total of 15 published datasets. The procedure does not adjoin raw data sets, but instead combines the binary-coded factors of the trees, each tree from a different data set, together. This allows the combining of data that are only available as pair-wise distances with data obtained directly from characters of the organisms. It economizes the analysis of combined nucleotide sequence data which can be very large, and preserves information for each kind of data in the combination. The procedure allows for missing data as well, and can be regarded as a new consensus method - mathematical properties have yet to be investigated. The desirability of combining gene trees, obtained from molecular data, to enable the inference of species trees is discussed in light of using this procedure.

In the second half of the twentieth century, gene sequences have been used to study their evolution as well as the history of species. A decade ago, progress in sequencing techniques provided the opportunity to use whole genome sequences for reconstructing species phylogeny. Several phylogenomic methods have been used to exploit these large amounts of data, and those that are based on homologous or orthologous characters have been favoured. Among these, the supertree and supermatrix approaches have been very successful at resolving parts of the tree of life. However, these methods discard a great proportion of the evolutionary information present in genomes. New integrative models of genome evolution could make a better use of whole genome sequences and thus improve the resolution of the tree of life. Key concepts Genomes contain a very large amount of information relevant for reconstructing their history and the history of species. Among phylogenomic methods, only those based on homologous/orthologous characters can reconstruct a species tree. Rare genomic changes, supertree and supermatrice methods have been the most extensively used. Genome-sized datasets have permitted confirming key phylogenies, and have also provided new insights into important parts of the tree of life. New methods that combine different types of genomic information could further improve the resolution of the tree of life. Keywords: phylogenomics; evolution; gene duplication; lateral gene transfer; trans-specific polymorphisms

This data set represents a comprehensive, dated phylogeny of a large European flora comprising the vascular plants of the British Isles, Germany, The Netherlands, and Switzerland, totaling 4685 species. The phylogeny thus encompasses all species in the trait databases BIOLFLOR, PLANTATT, and BioBase 2003. The topology of the phylogentic tree is based on a backbone family phylogeny of the Angiosperm Phylogeny Group III. Subsequently, partial phylogenetic subtrees derived from a total of 518 recent molecular studies were manually pruned onto the backbone tree, using multi-gene consensus topologies if possible. Similarly, 1103 internal nodes and the root node were dated based on 261 recent studies. Finally, an ultrametric tree was calculated by placing undated nodes evenly between dated nodes. The phylogeny provides a reference data set for comparative analyses of trait correlations, trait evolution, trait based ecological processes, community assembly, or other phylogenetically informed analyses across a la...

Although it is implicit that interactions between species depend on their traits, studies on the probability of finding related species in a community are in their infancy. Community composition and species richness of predaceous diving beetles (Dytiscidae: Coleoptera) have been used as indicators of freshwater ecosystem function yet no incorporation of phylogenetic relationships of coexisting dytiscids has been attempted to date. Improved knowledge of phylogenetic relationships and phylogenetic community structure analysis methods may provide additional insight into the relationships between community composition and species richness, thus impacting our interpretation of aquatic indicator species metrics. Here, we use museum records of dytiscid beetles in 53 lakes of Alberta, Canada to: (1) compile a supertree of dytiscid beetles that live in the province, (2) examine whether coexisting dytiscids tend to be more or less related than expected by chance, and (3) examine whether phylogenetic structuring depends on species richness or mean size of coexisting species. We find that, although the majority of dytiscid assemblages exhibited phylogenetic clustering, the extent to which this occurred depended on the mean size of dytiscids. We discuss the potential mechanisms and implications of the observed patterns in phylogenetic clustering, along with data that would further improve our understanding of community dynamics in dytiscid beetles.

Despite the biological and economic importance of the Cetartiodactyla, the phylogeny of this clade remains controversial. Using the supertree approach of matrix representation with parsimony, we present the first phylogeny to include all 290 extant species of the Cetacea (whales and dolphins) and Artiodactyla (even-toed hoofed mammals). At the family-level, the supertree is fully resolved. For example, the relationships among the Ruminantia appear as (((Cervidae, Moschidae) Bovidae) (Giraffidae, Antilocapridae) Tragulidae). However, due to either lack of phylogenetic study or contradictory information, polytomies occur within the clades Sus, Muntiacus, Cervus, Delphinidae, Ziphiidae and Bovidae. Complete species-level phylogenies are necessary for both illustrating and analysing biological, geographical and ecological patterns in an evolutionary framework. The present species-level tree of the Cetartiodactyla provides the first opportunity to examine comparative hypotheses across entirely aquatic and terrestrial species within a single mammalian order.